Class Examples

Table of Contents

• Overview
• IMP.algebra
• IMP.atom
• IMP.base
• IMP.container
• IMP.core
• IMP.display
• IMP.domino
• IMP.em
• IMP.em2d
• IMP.example
• IMP.gsl
• IMP.kernel
• IMP.kmeans
• IMP.misc
• IMP.modeller
• IMP.parallel
• IMP.rmf
• IMP.rotamer
• IMP.saxs
• IMP.score_functor
• IMP.statistics

Overview

Examples that use a given class:

See also Factory Index, Argument Index, Class Examples, Function Examples

IMP.algebra

Class	Examples
IMP::algebra::BoundingBoxD	algebra/geometry.py, container/filter_close_pairs.py, core/incremental_mc.py, core/optimize_balls.py, core/rigid_collisions.py, display/basic_geometry.py, domino/merge_tree.py, domino/multiscale.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, em/cube.py, example/range_restriction.py, kernel/nup84.py, kernel/setup.py, misc/decay.py, restrainer/rigid_body_and_excluded_volume_restraint.py, rmf/geometry.py, rmf/simulation.py
IMP::algebra::Cylinder3D	algebra/geometry.py, display/displaying_ensembles.py
IMP::algebra::ReferenceFrame3D	atom/cg_pdb.py, atom/rigid_brownian_dynamics.py, domino/rigid_body_excluded_volume.py, em/analyze_convergence.py, restrainer/rigid_body_and_excluded_volume_restraint.py
IMP::algebra::Segment3D	algebra/geometry.py, display/displaying_ensembles.py
IMP::algebra::SphereD	algebra/geometry.py, algebra/grid_space.py, atom/rigid_brownian_dynamics.py, container/filter_close_pairs.py, core/XYZR_Decorator.py, core/connectivity_restraint.py, core/optimize_balls.py, core/restrain_in_sphere.py, display/basic_geometry.py, domino/merge_tree.py, em/analyze_convergence.py, em/cube.py, kernel/setup.py, statistics/kmeans.py
IMP::algebra::Transformation3D	atom/cg_pdb.py, atom/markers.py, atom/rigid_brownian_dynamics.py, core/rigid_collisions.py, core/symmetry.py, domino/rigid_body_excluded_volume.py, em2d/optimize_em2d_with_montecarlo.py, em/local_fitting.py, restrainer/rigid_body_and_excluded_volume_restraint.py
IMP::algebra::VectorD	algebra/grid_space.py, atom/cg_pdb.py, atom/dope_and_excluded_volume.cpp, atom/markers.py, atom/rigid_brownian_dynamics.py, container/filter_close_pairs.py, container/restrain_in_sphere.py, core/XYZR_Decorator.py, core/XYZ_Decorator.py, core/connectivity_restraint.py, core/incremental_mc.py, core/ms_connectivity_restraint.py, core/optimize_balls.py, core/restrain_in_sphere.py, core/rigid_collisions.py, core/simple.cpp, core/simple.py, core/symmetry.py, display/basic_geometry.py, domino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, em/cube.py, example/range_restriction.py, gsl/simplex.py, kernel/nup84.py, kernel/setup.py, misc/decay.py, parallel/tasks.py, restrainer/rigid_body_and_excluded_volume_restraint.py, rmf/geometry.py, rmf/simulation.py, statistics/kmeans.py

IMP.atom

Class	Examples
IMP::atom::ATOMPDBSelector	em2d/optimize_em2d_with_montecarlo.py, kernel/dependency_graph.py, kernel/nup84.py
IMP::atom::AngleSingletonScore	atom/charmm_forcefield_verbose.py
IMP::atom::Atom	atom/dope_and_excluded_volume.cpp
IMP::atom::AtomType
IMP::atom::BondSingletonScore	atom/charmm_forcefield_verbose.py, atom/load_protein_restrain_bonds.py
IMP::atom::BondedPairFilter	container/nonbonded_interactions.py
IMP::atom::BrownianDynamics	atom/rigid_brownian_dynamics.py, misc/decay.py, rmf/simulation.py
IMP::atom::CAlphaPDBSelector	display/displaying_ensembles.py, domino/rigid_body_excluded_volume.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py, restrainer/simple_connectivity_on_rigid_bodies.py, restrainer/simple_excluded_volume.py
IMP::atom::CHARMMStereochemistryRestraint	atom/charmm_forcefield.py
IMP::atom::CHARMMTopology	atom/structure_from_sequence.py
IMP::atom::Chain	atom/cg_pdb.py, atom/dope_and_excluded_volume.cpp, atom/molecular_hierarchy.py, display/displaying_ensembles.py, kernel/dependency_graph.py, kernel/nup84.py
IMP::atom::DihedralSingletonScore	atom/charmm_forcefield_verbose.py
IMP::atom::DopePairScore	atom/assess_dope.py
IMP::atom::ForceSwitch	atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py
IMP::atom::Hierarchy	core/rigid_bodies.py
IMP::atom::HierarchyGeometry	atom/markers.py, atom/rigid_brownian_dynamics.py, domino/rigid_body_excluded_volume.py
IMP::atom::ImproperSingletonScore	atom/charmm_forcefield_verbose.py
IMP::atom::LennardJonesPairScore	atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py
IMP::atom::NonWaterNonHydrogenPDBSelector	atom/assess_dope.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, saxs/profile.py, saxs/profile_fit.py
IMP::atom::NonWaterPDBSelector	em/fit_restraint.py, em/pdb2density.py
IMP::atom::ProteinLigandAtomPairScore	atom/score_protein_with_ligand.py
IMP::atom::Residue	atom/dope_and_excluded_volume.cpp, atom/edit_molecular_hierarchy.py, rmf/multiresolution.py
IMP::atom::SameResiduePairFilter	atom/assess_dope.py
IMP::atom::Selection	atom/markers.py, atom/rigid_brownian_dynamics.py, display/displaying_ensembles.py, kernel/dependency_graph.py, kernel/nup84.py
IMP::atom::SelectionGeometry	atom/markers.py
IMP::atom::StereochemistryPairFilter	atom/charmm_forcefield_verbose.py
IMP::atom::WritePDBOptimizerState	em2d/optimize_em2d_with_montecarlo.py

IMP.base

Class	Examples
IMP::base::Array	atom/dope_and_excluded_volume.cpp, domino/marina_party.py
IMP::base::CreateLogContext	base/log.py
IMP::base::Index	atom/dope_and_excluded_volume.cpp
IMP::base::ModelException	core/rigid_collisions.py
IMP::base::Object	base/log.py
IMP::base::SetLogState	base/log.py, domino/restraint_cache.py, kernel/dependency_graph.py
IMP::base::Vector	atom/dope_and_excluded_volume.cpp, core/rigid_collisions.py, em/local_fitting.py, restrainer/simple_connectivity_on_molecules.py, restrainer/simple_connectivity_on_rigid_bodies.py, restrainer/simple_em_fit.py, restrainer/simple_excluded_volume.py, saxs/profile_fit.py

IMP.container

Class	Examples
IMP::container::CloseBipartitePairContainer	container/bipartite_nonbonded_interactions.py, container/filter_close_pairs.py
IMP::container::ClosePairContainer	atom/assess_dope.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, container/filter_close_pairs.py, container/nonbonded_interactions.py, core/excluded_volume.py, core/rigid_collisions.py, kernel/basic_optimization.py, kernel/chain.py
IMP::container::ConnectingPairContainer	container/connectivity.py
IMP::container::ConsecutivePairContainer	domino/restraint_cache.py, kernel/chain.py
IMP::container::ConsecutivePairFilter	kernel/chain.py
IMP::container::ExclusiveConsecutivePairContainer	core/optimize_balls.py
IMP::container::ExclusiveConsecutivePairFilter	core/optimize_balls.py
IMP::container::ListPairContainer	domino/custom_filter.py, domino/interactive.py, domino/interactive_with_containers.py, domino/merge_tree.py, domino/six_particles_optimization.py
IMP::container::ListSingletonContainer	atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/load_protein_restrain_bonds.py, atom/rigid_brownian_dynamics.py, container/bipartite_nonbonded_interactions.py, container/connectivity.py, container/filter_close_pairs.py, container/nonbonded_interactions.py, core/incremental_mc.py, core/restrain_diameter.py, core/rigid_collisions.py, core/symmetry.py, display/display_log.py, display/show_particles_as_spheres.py, domino/rigid_body_excluded_volume.py, em2d/optimize_em2d_with_montecarlo.py, example/range_restriction.py, kernel/chain.py, kernel/setup.py
IMP::container::PairsRestraint	atom/assess_dope.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, container/bipartite_nonbonded_interactions.py, container/nonbonded_interactions.py, core/excluded_volume.py, core/optimize_balls.py, core/rigid_collisions.py, domino/custom_filter.py, domino/interactive.py, domino/interactive_with_containers.py, domino/merge_tree.py, domino/restraint_cache.py, domino/six_particles_optimization.py, kernel/basic_optimization.py, kernel/chain.py, misc/decay.py, rmf/simulation.py
IMP::container::SingletonsConstraint	example/range_restriction.py
IMP::container::SingletonsRestraint	atom/charmm_forcefield_verbose.py, atom/load_protein_restrain_bonds.py, container/restrain_in_sphere.py, core/incremental_mc.py, core/optimize_balls.py, misc/decay.py, rmf/simulation.py

IMP.core

Class	Examples
IMP::core::BallMover	core/incremental_mc.py, core/optimize_balls.py, core/restrain_minimum_distance.py, display/display_log.py, kernel/nup84.py
IMP::core::ChildrenRefiner	core/connectivity_restraint.py, core/cover_particles.py
IMP::core::CoinFlipPairPredicate	misc/decay.py
IMP::core::ConjugateGradients	container/bipartite_nonbonded_interactions.py, container/nonbonded_interactions.py, core/optimize_balls.py, core/restrain_diameter.py, core/rigid_collisions.py, core/simple.py, core/symmetry.py, em/analyze_convergence.py
IMP::core::ConnectivityRestraint	core/connectivity_restraint.py, restrainer/simple_connectivity_on_molecules.py, restrainer/simple_connectivity_on_rigid_bodies.py
IMP::core::DiameterRestraint	core/restrain_diameter.py, restrainer/simple_diameter.py
IMP::core::DistancePairScore	core/ms_connectivity_restraint.py, core/pair_restraint.py, core/simple.py, kernel/basic_optimization.py
IMP::core::DistanceRestraint	domino/domino_approach.py, em2d/optimize_em2d_with_montecarlo.py, gsl/simplex.py, modeller/imp_restraints_in_modeller.py, parallel/tasks.py, restrainer/simple_distance.py
IMP::core::EdgePairsGeometry	container/connectivity.py
IMP::core::ExcludedVolumeRestraint	atom/rigid_brownian_dynamics.py, core/excluded_volume.py, core/incremental_mc.py, core/optimize_balls.py, core/symmetry.py, display/display_log.py, domino/rigid_body_excluded_volume.py, misc/decay.py, restrainer/rigid_body_and_excluded_volume_restraint.py, restrainer/simple_excluded_volume.py, rmf/simulation.py
IMP::core::GenericAttributeSingletonScore	domino/multiscale.py
IMP::core::GenericBoundingBox3DSingletonScore	core/incremental_mc.py, core/optimize_balls.py, misc/decay.py, rmf/simulation.py
IMP::core::GenericDistanceToSingletonScore	container/restrain_in_sphere.py, core/restrain_in_sphere.py, core/simple.py, domino/custom_filter.py, domino/multiscale.py, domino/six_particles_optimization.py
IMP::core::GridClosePairsFinder	domino/merge_tree.py
IMP::core::Harmonic	atom/charmm_forcefield_verbose.py, atom/load_protein_restrain_bonds.py, core/pair_restraint.py, core/simple.py, domino/domino_approach.py, domino/multiscale.py, em2d/optimize_em2d_with_montecarlo.py, gsl/simplex.py, modeller/imp_restraints_in_modeller.py, parallel/tasks.py
IMP::core::HarmonicDistancePairScore	core/optimize_balls.py, domino/custom_filter.py, domino/interactive.py, domino/interactive_with_containers.py, domino/six_particles_optimization.py, kernel/chain.py, rotamer/rotamer_pdb2.py
IMP::core::HarmonicLowerBound	container/bipartite_nonbonded_interactions.py, core/excluded_volume.py, core/rigid_collisions.py, kernel/basic_optimization.py
IMP::core::HarmonicSphereDistancePairScore	core/restrain_minimum_distance.py, domino/multiscale.py
IMP::core::HarmonicUpperBound	container/restrain_in_sphere.py, core/connectivity_restraint.py, core/incremental_mc.py, core/ms_connectivity_restraint.py, core/optimize_balls.py, core/restrain_diameter.py, core/restrain_in_sphere.py, display/displaying_ensembles.py, domino/custom_filter.py, domino/six_particles_optimization.py, misc/decay.py, rmf/simulation.py
IMP::core::HarmonicUpperBoundSphereDistancePairScore	domino/restraint_cache.py, misc/decay.py, rmf/simulation.py
IMP::core::HierarchyTraits	core/custom_hierarchy.py
IMP::core::IncrementalScoringFunction	core/incremental_mc.py, core/optimize_balls.py, kernel/nup84.py
IMP::core::KClosePairsPairScore	core/connectivity_restraint.py, core/restrain_minimum_distance.py, display/displaying_ensembles.py
IMP::core::LeavesRefiner	display/displaying_ensembles.py, em/local_fitting.py
IMP::core::MCCGSampler	kernel/basic_optimization.py, kernel/chain.py
IMP::core::MSConnectivityRestraint	core/ms_connectivity_restraint.py
IMP::core::MonteCarlo	core/incremental_mc.py, core/optimize_balls.py, core/restrain_minimum_distance.py, display/display_log.py, em2d/optimize_em2d_with_montecarlo.py, kernel/nup84.py
IMP::core::PairRestraint	core/pair_restraint.py, core/restrain_minimum_distance.py, core/simple.py, domino/marina_party.py, domino/multiscale.py, kernel/chain.py
IMP::core::RestraintsScoringFunction	core/optimize_balls.py, rmf/simulation.py
IMP::core::RigidBody	restrainer/rigid_body_and_excluded_volume_restraint.py
IMP::core::RigidBodyMover	em2d/optimize_em2d_with_montecarlo.py, kernel/nup84.py
IMP::core::RigidClosePairsFinder	core/rigid_collisions.py
IMP::core::RigidMember	display/displaying_ensembles.py, domino/rigid_body_excluded_volume.py, em/local_fitting.py
IMP::core::SerialMover	core/incremental_mc.py, core/optimize_balls.py, kernel/nup84.py
IMP::core::SingletonConstraint	core/symmetry.py
IMP::core::SingletonRestraint	core/restrain_in_sphere.py, core/simple.py, domino/multiscale.py, domino/six_particles_optimization.py
IMP::core::SoftSpherePairScore	container/nonbonded_interactions.py, core/optimize_balls.py, domino/merge_tree.py, kernel/chain.py, kernel/nup84.py
IMP::core::SphereDistancePairScore	container/bipartite_nonbonded_interactions.py, core/connectivity_restraint.py, core/excluded_volume.py, core/rigid_collisions.py, display/displaying_ensembles.py
IMP::core::TableRefiner	core/restrain_minimum_distance.py, em/analyze_convergence.py
IMP::core::TransformationSymmetry	core/symmetry.py
IMP::core::TypedPairScore
IMP::core::XYZ	atom/score_protein_with_ligand.py, core/restrain_diameter.py, core/simple.cpp, core/symmetry.py, display/displaying_ensembles.py, domino/custom_filter.py, domino/six_particles_optimization.py, kernel/nup84.py, rmf/pdb.py, rotamer/rotamer_pdb.py
IMP::core::XYZDerivativeGeometry	em/analyze_convergence.py
IMP::core::XYZR	atom/markers.py, core/optimize_balls.py, display/show_particles_as_spheres.py, kernel/nup84.py
IMP::core::XYZRGeometry	atom/markers.py, core/incremental_mc.py, core/optimize_balls.py, display/displaying_ensembles.py, domino/multiscale.py, kernel/chain.py
IMP::core::XYZRsGeometry	display/display_log.py, display/show_particles_as_spheres.py

IMP.display

Class	Examples
IMP::display::BoundingBoxGeometry	core/optimize_balls.py, display/basic_geometry.py, misc/decay.py, rmf/geometry.py, rmf/simulation.py
IMP::display::ChimeraWriter	container/connectivity.py, display/display_log.py, display/show_particles_as_spheres.py, em/cube.py, kernel/chain.py
IMP::display::Color	atom/markers.py, display/display_log.py, display/displaying_ensembles.py, display/show_particles_as_spheres.py, domino/multiscale.py
IMP::display::CylinderGeometry	display/displaying_ensembles.py
IMP::display::PointGeometry	domino/multiscale.py
IMP::display::PymolWriter	atom/markers.py, atom/rigid_brownian_dynamics.py, core/incremental_mc.py, core/optimize_balls.py, display/basic_geometry.py, display/displaying_ensembles.py, domino/multiscale.py, domino/rigid_body_excluded_volume.py, em/analyze_convergence.py
IMP::display::ReferenceFrameGeometry	display/displaying_ensembles.py
IMP::display::SphereGeometry	display/basic_geometry.py, em/analyze_convergence.py, em/cube.py
IMP::display::WriteOptimizerState	display/display_log.py
IMP::display::Writer	display/show_particles_as_spheres.py

IMP.domino

Class	Examples
IMP::domino::Assignment	domino/save_assignments.py
IMP::domino::BranchAndBoundAssignmentsTable	domino/custom_filter.py, domino/interactive_with_containers.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::DominoSampler	domino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/marina_party.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::ExclusionSubsetFilterTable	domino/custom_filter.py, domino/interactive_with_containers.py, domino/marina_party.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::ListSubsetFilterTable	domino/marina_party.py, domino/multiscale.py
IMP::domino::ParticleStates	domino/marina_party.py
IMP::domino::ParticleStatesTable	domino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/marina_party.py, domino/merge_tree.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::ReadAssignmentContainer	domino/save_assignments.py
IMP::domino::ReadHDF5AssignmentContainer	domino/interactive_with_containers.py
IMP::domino::RestraintCache	domino/custom_filter.py, domino/interactive_with_containers.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::RestraintScoreSubsetFilterTable	domino/custom_filter.py, domino/interactive_with_containers.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/six_particles_optimization.py
IMP::domino::RigidBodyStates	domino/rigid_body_excluded_volume.py
IMP::domino::Subset	domino/multiscale.py, domino/restraint_cache.py, domino/save_assignments.py
IMP::domino::SubsetFilter	domino/custom_filter.py
IMP::domino::SubsetFilterTable	domino/custom_filter.py
IMP::domino::WriteAssignmentContainer	domino/save_assignments.py
IMP::domino::WriteHDF5AssignmentContainer	domino/interactive_with_containers.py
IMP::domino::XYZStates	domino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/merge_tree.py, domino/multiscale.py, domino/restraint_cache.py, domino/six_particles_optimization.py

IMP.em

Class	Examples
IMP::em::FitRestraint	em/analyze_convergence.py, em/fit_restraint.py, restrainer/em_restraint.py, restrainer/simple_em_fit.py
IMP::em::MRCReaderWriter	em/analyze_convergence.py, em/fit_restraint.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py, em/pdb2density.py
IMP::em::SampledDensityMap	em/analyze_convergence.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py

IMP.em2d

Class	Examples
IMP::em2d::EM2DScore	em2d/optimize_em2d_with_montecarlo.py
IMP::em2d::Em2DRestraint	em2d/optimize_em2d_with_montecarlo.py
IMP::em2d::SpiderImageReaderWriter	em2d/optimize_em2d_with_montecarlo.py

IMP.example

Class	Examples
IMP::example::ExampleSingletonModifier	example/range_restriction.py

IMP.gsl

Class	Examples
IMP::gsl::Simplex	gsl/simplex.py

IMP.kernel

Class	Examples
IMP::kernel::ConfigurationSet	kernel/nup84.py
IMP::kernel::Decorator	domino/marina_party.py
IMP::kernel::Key	container/filter_close_pairs.py, domino/marina_party.py, kernel/write_a_restraint.py, kernel/write_an_optimizer_state.py, restrainer/simple_distance.py, restrainer/simple_em_fit.py
IMP::kernel::Model	atom/assess_dope.py, atom/cg_pdb.py, atom/charmm_forcefield.py, atom/charmm_forcefield_verbose.py, atom/dope_and_excluded_volume.cpp, atom/edit_molecular_hierarchy.py, atom/load_protein_restrain_bonds.py, atom/markers.py, atom/molecular_hierarchy.py, atom/rigid_brownian_dynamics.py, atom/score_protein_with_ligand.py, atom/structure_from_sequence.py, container/bipartite_nonbonded_interactions.py, container/connectivity.py, container/filter_close_pairs.py, container/nonbonded_interactions.py, core/XYZR_Decorator.py, core/XYZ_Decorator.py, core/connectivity_restraint.py, core/cover_particles.py, core/custom_hierarchy.py, core/incremental_mc.py, core/ms_connectivity_restraint.py, core/optimize_balls.py, core/randomize_rigid_body.py, core/restrain_diameter.py, core/restrain_in_sphere.py, core/restrain_minimum_distance.py, core/rigid_bodies.py, core/rigid_collisions.py, core/simple.cpp, core/simple.py, core/symmetry.py, display/display_log.py, display/displaying_ensembles.py, display/show_particles_as_spheres.py, domino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/marina_party.py, domino/merge_tree.py, domino/multiscale.py, domino/restraint_cache.py, domino/rigid_body_excluded_volume.py, domino/save_assignments.py, domino/six_particles_optimization.py, em2d/clustering_of_pdb_models.py, em2d/collision_cross_section.py, em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, em/fit_restraint.py, em/generate_density_map_of_fixed_dimension.py, em/local_fitting.py, em/pdb2density.py, example/range_restriction.py, gsl/simplex.py, kernel/chain.py, kernel/dependency_graph.py, kernel/graph.py, kernel/nup84.py, kernel/setup.py, kernel/write_a_restraint.py, kernel/write_an_optimizer_state.py, misc/decay.py, modeller/imp_restraints_in_modeller.py, modeller/load_modeller_model.py, modeller/modeller_restraints_in_imp.py, parallel/tasks.py, restrainer/simple_connectivity_on_molecules.py, restrainer/simple_connectivity_on_rigid_bodies.py, restrainer/simple_diameter.py, restrainer/simple_distance.py, restrainer/simple_em_fit.py, restrainer/simple_excluded_volume.py, rmf/link.py, rmf/multiresolution.py, rmf/pdb.py, rmf/simulation.py, rotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py, saxs/profile.py, saxs/profile_fit.py
IMP::kernel::OptimizerState	em2d/optimize_em2d_with_montecarlo.py, kernel/write_an_optimizer_state.py
IMP.kernel.OptionParser	rotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py
IMP::kernel::PairPredicate	container/filter_close_pairs.py
IMP::kernel::PairScore	domino/marina_party.py
IMP::kernel::Particle	atom/molecular_hierarchy.py, atom/rigid_brownian_dynamics.py, container/filter_close_pairs.py, core/XYZR_Decorator.py, core/connectivity_restraint.py, core/custom_hierarchy.py, core/incremental_mc.py, core/ms_connectivity_restraint.py, core/optimize_balls.py, core/randomize_rigid_body.py, core/rigid_collisions.py, core/simple.cpp, core/simple.py, core/symmetry.py, display/displaying_ensembles.py, domino/custom_filter.py, domino/domino_approach.py, domino/interactive.py, domino/interactive_with_containers.py, domino/marina_party.py, domino/merge_tree.py, domino/multiscale.py, domino/restraint_cache.py, domino/save_assignments.py, domino/six_particles_optimization.py, em/analyze_convergence.py, gsl/simplex.py, kernel/dependency_graph.py, kernel/graph.py, kernel/nup84.py, kernel/setup.py, kernel/write_a_restraint.py, misc/decay.py, parallel/tasks.py, restrainer/simple_distance.py, restrainer/simple_em_fit.py, rmf/multiresolution.py, rmf/simulation.py
IMP::kernel::Restraint	kernel/write_a_restraint.py
IMP::kernel::RestraintSet	em2d/optimize_em2d_with_montecarlo.py, em/analyze_convergence.py, kernel/write_an_optimizer_state.py
IMP::kernel::ScopedSetAttribute	core/optimize_balls.py

IMP.kmeans

Class	Examples
IMP::kmeans::KMeans	kmeans/kmeans_example.py

IMP.misc

Class	Examples
IMP::misc::DecayPairContainerOptimizerState	misc/decay.py

IMP.modeller

Class	Examples
IMP.modeller.IMPRestraints	modeller/imp_restraints_in_modeller.py
IMP.modeller.ModelLoader	modeller/imp_restraints_in_modeller.py, modeller/load_modeller_model.py, modeller/modeller_restraints_in_imp.py
IMP.modeller.ModellerRestraints	modeller/modeller_restraints_in_imp.py

IMP.parallel

Class	Examples
IMP.parallel.LocalSlave	parallel/local_distance.py
IMP.parallel.Manager	parallel/local_distance.py

IMP.rmf

Class	Examples
IMP::rmf::SaveOptimizerState	misc/decay.py, rmf/simulation.py

IMP.rotamer

Class	Examples
IMP::rotamer::RotamerCalculator	rotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py
IMP::rotamer::RotamerLibrary	rotamer/rotamer_pdb2.py, rotamer/rotamer_pdb.py

IMP.saxs

Class	Examples
IMP::saxs::Profile	saxs/profile.py, saxs/profile_fit.py
IMP::saxs::RadialDistributionFunction	saxs/profile.py
IMP::saxs::Restraint	restrainer/saxs_restraint.py
IMP::saxs::SolventAccessibleSurface	saxs/profile_fit.py

IMP.score_functor

Class	Examples
IMP::score_functor::AddScores	atom/dope_and_excluded_volume.cpp
IMP::score_functor::DistancePairScore	atom/dope_and_excluded_volume.cpp
IMP::score_functor::Dope	atom/dope_and_excluded_volume.cpp
IMP::score_functor::HarmonicLowerBound	atom/dope_and_excluded_volume.cpp
IMP::score_functor::SphereDistance	atom/dope_and_excluded_volume.cpp

IMP.statistics

Class	Examples
IMP::statistics::ConfigurationSetXYZEmbedding	kernel/basic_optimization.py, statistics/kmeans.py
IMP::statistics::Metric	statistics/write_a_metric.py
IMP::statistics::ParticleEmbedding	statistics/kmeans.py
IMP::statistics::VectorDEmbedding	statistics/kmeans.py